Introduction

We present CisGenome, a software system for analyzing genome-wide chromatin immunoprecipitation (ChIP) data. CisGenome is designed to meet all basic needs of ChIP data analyses, including visualization, data normalization, peak detection, false discovery rate computation, gene-peak association, and sequence and motif analysis. In addition to implementing previously published ChIP-microarray (ChIP-chip) analysis methods, the software contains statistical methods designed specifically for ChlP sequencing (ChIP-seq) data obtained by coupling ChIP with massively parallel sequencing. The modular design of CisGenome enables it to support interactive analyses through a graphic user interface as well as customized batch-mode computation for advanced data mining. A built-in browser allows visualization of array images, signals, gene structure, conservation, and DNA sequence and motif information. We demonstrate the use of these tools by a comparative analysis of ChIP-chip and ChIP-seq data for the transcription factor NRSF/REST, a study of ChIP-seq analysis with or without a negative control sample, and an analysis of a new motif in Nanog- and Sox2-binding regions.

Publications

  1. An integrated software system for analyzing ChIP-chip and ChIP-seq data.
    Cite this
    Ji H, Jiang H, Ma W, Johnson DS, Myers RM, Wong WH, 2008-11-01 - Nature biotechnology

Credits

  1. Hongkai Ji
    Developer

    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, United States of America

  2. Hui Jiang
    Developer

  3. Wenxiu Ma
    Developer

  4. David S Johnson
    Developer

  5. Richard M Myers
    Developer

  6. Wing H Wong
    Investigator

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Summary
AccessionBT000553
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC, C++
User InterfaceTerminal Command Line
Download Count0
Submitted ByWing H Wong